SMTL ID : 1c9u.1

CRYSTAL STRUCTURE OF THE SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE IN COMPLEX WITH PQQ

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.251, A.269, Y.271, D.273, E.309 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.269, A:Y.271, A:E.309, H2O.1, H2O.2 CA.2: 3 residues within 4Å: Chain A: E.253, Y.263, V.268 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.253, A:Y.263, H2O.1, H2O.2, H2O.3 CA.3: 4 residues within 4Å: Chain A: R.228, G.247, P.248 Ligands: PQQ.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.247, A:P.248, H2O.2, H2O.8 CA.8: 4 residues within 4Å: Chain B: A.269, Y.271, D.273, E.309 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.271, B:D.273, B:E.309, B:E.309, H2O.11 CA.9: 2 residues within 4Å: Chain B: E.253, Y.263 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.253, B:Y.263, H2O.11, H2O.12, H2O.12 CA.10: 3 residues within 4Å: Chain B: G.247, P.248 Ligands: PQQ.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.247, B:P.248, H2O.13, H2O.22

2 x PQQ: PYRROLOQUINOLINE QUINONE(Non-covalent)

PQQ.4: 18 residues within 4Å: Chain A: Q.76, H.144, R.228, N.229, Q.231, Q.246, G.247, P.248, Y.343, W.346, T.348, A.350, L.376, K.377, R.406, R.408 Ligands: CA.3, GOL.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.343, A:A.350, A:K.377 Hydrogen bonds: A:R.228, A:R.228, A:N.229, A:Q.231, A:Q.246, A:T.348, A:R.406 Water bridges: A:G.247, A:A.350, A:R.408, A:R.408, A:R.408 Salt bridges: A:K.377, A:R.406, A:R.406, A:R.408 PQQ.11: 18 residues within 4Å: Chain B: Q.76, H.144, R.228, N.229, Q.231, Q.246, G.247, P.248, Y.343, W.346, T.348, A.350, L.376, K.377, R.406, R.408 Ligands: CA.10, GOL.12 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.343, B:A.350 Hydrogen bonds: B:R.228, B:R.228, B:N.229, B:Q.231, B:Q.246, B:T.348, B:R.406 Water bridges: B:R.408, B:R.408, B:R.408 Salt bridges: B:K.377, B:R.406, B:R.408

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: L.169, Y.343, W.346 Ligands: PQQ.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.343 Water bridges: A:Q.168 GOL.6: 1 residues within 4Å: Chain A: K.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.299 GOL.7: 8 residues within 4Å: Chain A: P.3, L.4, D.335, C.345, W.346, P.347, R.378, Q.430 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.335, A:D.335, A:R.378, A:R.378, A:Q.430, A:Q.430 GOL.12: 2 residues within 4Å: Chain B: Y.343 Ligands: PQQ.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oubrie, A. et al., Structure and mechanism of soluble quinoprotein glucose dehydrogenase. EMBO J. (1999)

Release Date

2000-02-04

Peptides

SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE

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